Cell-Type-Specific Surfaceome Profiling of 100-500 Isolated Cells using a Droplet-Based Magnetic Affinity Purification System

ABSTRACT Cell surface proteins (CSPs) represent an important source of biomarkers and therapeutic targets. However, due to the inherent sensitivity limitations of existing technologies, tissue and cell-type-specific surfaceomes remain poorly characterized, especially in the context of human diseases. Herein, we develop nanoMAPS (nanoscale Magnetic Affinity Purification System), a miniaturized proteomic sample preparation method for surfaceome profiling of as few as 100-500 cells (1000× to 100,000× lower than existing technologies). We demonstrate that the miniaturization of magnetic bead-based affinity purification inside a single droplet can efficiently improve the recovery of surface proteins and reduce non-specific absorption of intracellular proteins. By applying nanoMAPS to human immune cells isolated from PBMCs, we demonstrate robust identification of both well-known cell-type-specific surface markers and candidate proteins. We establish nanoMAPS as a promising platform to expand surface proteomics from cultured cells to primary cells isolated from patients or mouse models. Competing Interest Statement All authors are employees of Genentech, Inc., a member of the Roche group. DATA AVAILABILITY The mass spectrometry raw data have been deposited to the ProteomeXchange Consortium via the MassIVE partner repository with dataset identifier MSV000097303.